Ignore graph links for simple graphs

ablab · Jun 5, 2023 · b919f2c · b919f2c
1 parent b92b0df
commit b919f2c
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Showing 3 changed files with 15 additions and 7 deletions.
diff --git a/assembler/src/common/sequence/sequence.hpp b/assembler/src/common/sequence/sequence.hpp
@@ -73,7 +73,7 @@ class Sequence {
         size_t bytes_size = DataSize(size_);
         ST *bytes = data_->data();
 
-        VERIFY(is_dignucl(s[0]) || is_nucl(s[0]));
+        //VERIFY(is_dignucl(s[0]) || is_nucl(s[0]));
 
         // Which symbols does our string contain : 0123 or ACGT?
         bool digit_str = is_dignucl(s[0]);

diff --git a/assembler/src/projects/splitter/main.cpp b/assembler/src/projects/splitter/main.cpp
@@ -161,9 +161,9 @@ gfa::GFAReader ReadGraph(const gcfg &cfg,
             FATAL_ERROR("Unknown graph representation type");
         case GraphType::Multiplexed: {
             gfa::GFAReader gfa(cfg.graph);
-            INFO("GFA segments: " << gfa.num_edges() << ", links: " << gfa.num_links() << ", paths: "
-                                  << gfa.num_paths());
             gfa.to_graph(graph, id_mapper);
+	    INFO("GFA segments: " << gfa.num_edges() << ", links: " << gfa.num_links() << ", paths: "
+			                                      << gfa.num_paths());
             return gfa;
         }
     }

diff --git a/assembler/src/projects/splitter/path_extractor.cpp b/assembler/src/projects/splitter/path_extractor.cpp
@@ -121,10 +121,18 @@ PathExtractor::ScaffoldLinks PathExtractor::GetScaffoldLinks(const VertexResults
         const auto &vertex_result = vertex_entry.second;
         auto vertex = vertex_entry.first;
         DEBUG("Updating link storage");
-        for (const debruijn_graph::LinkId &link_id: graph_.links(vertex)) {
-            auto &link = graph_.link(link_id);
-            TRACE(link.link.first.int_id() << "," << link.link.second.int_id() << "," << link_id);
-            vertex_link_storage[link.link.first].insert(link.link.second);
+        if (graph_.is_complex(vertex)) {
+            for (const debruijn_graph::LinkId &link_id: graph_.links(vertex)) {
+                auto &link = graph_.link(link_id);
+                TRACE(link.link.first.int_id() << "," << link.link.second.int_id() << "," << link_id);
+                vertex_link_storage[link.link.first].insert(link.link.second);
+            }
+        } else {
+            for (const auto &in_edge: graph_.IncomingEdges(vertex)) {
+                for (const auto &out_edge: graph_.OutgoingEdges(vertex)) {
+                    vertex_link_storage[in_edge].insert(out_edge);
+                }
+            }
         }
         DEBUG("Constructing path map");
         for (const auto &entry: vertex_result.supported_pairs) {